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Biomedical subjects

Tomoji Kawai

Publications and source records attributed to Tomoji Kawai.

At least 19 recordsLinked to original sources
PubMed2007

Peptide-nucleic acid-modified ion-sensitive field-effect transistor-based biosensor for direct detection of DNA hybridization.

Here, we report the development of a peptide-nucleic acid (PNA)-modified ion-sensitive field-effect transistor (IS-FET)-based biosensor that takes advantage of the change in the surface potential upon hybridization of a negatively charged DNA. PNA was immobilized on a silicon nitride gate insulator by an addition reaction between a maleimide group introduced on the gate surface, the succinimide group of N-(6-maleimidocaproyloxy) succinimide, and the thiol group of the terminal cysteine in PNA. The surface was characterized after each step of the reaction by X-ray photoelectron spectroscopy analysis, and the kinetic analysis of the hybridization events was assessed by surface plasmon resonance. In addition, we measured the -potential before and after PNA-DNA hybridization in the presence of counterions to investigate the change in surface charge density at the surface-solution interface within the order of the Debye length. On the basis of the zeta-potential, the surface charge density, DeltaQ, calculated using the Grahame equation was approximately 4.0 x 10(-3) C/m2 and the estimated number of hybridized molecules was at least 1.7 x 10(11)/cm2. The I-V characteristics revealed that the PNA-DNA duplexes induce a positive shift in the threshold voltage, VT, and a decrease in the saturated drain current, ID. These results demonstrate that direct detection of DNA hybridization should be possible using a PNA-modified IS-FET-based biosensor. PNA is particularly advantageous for this system because it enables highly specific and selective binding at low ionic strength.

Base Sequence↗
PubMed2006

Photoconductive coaxial nanotubes of molecularly connected electron donor and acceptor layers.

Controlled self-assembly of a trinitrofluorenone-appended gemini-shaped amphiphilic hexabenzocoronene selectively formed nanotubes or microfibers with different photochemical properties. In these nanotubes, which are 16 nanometers in diameter and several micrometers long, a molecular layer of electron-accepting trinitrofluorenone laminates an electron-donating graphitic layer of pi-stacked hexabenzocoronene. The coaxial nanotubular structure allows photochemical generation of spatially separated charge carriers and a quick photoconductive response with a large on/off ratio greater than 10(4). In sharp contrast, the microfibers consist of a charge-transfer complex between the hexabenzocoronene and trinitrofluorenone parts and exhibit almost no photocurrent generation.

Journal Article↗
PubMed2006

Self-organized interconnect method for molecular devices.

Lack of an appropriate method for wiring molecules that have controlled functions and structures has been a barrier for the development of molecular devices. We developed an interconnect method to program three kinds of component molecules with their own functions and to wire a molecular device in a self-organized manner. By using the interconnect method we developed, we produced conductive wires and optical switching devices and have demonstrated their device functions. Our interconnect method allows us to control various molecular device characteristics by combining the three molecules.

Journal Article↗
PubMed2006

Electrochemical detection of 17beta-estradiol using DNA aptamer immobilized gold electrode chip.

An electrochemical detection method for chemical sensing has been developed using a DNA aptamer immobilized gold electrode chip. DNA aptamers specifically binding to 17beta-estradiol were selected by the SELEX (Systematic Evolution of Ligands by EXponential enrichment) process from a random ssDNA library, composed of approximately 7.2 x 10(14) DNA molecules. Gold electrode chips were employed to evaluate the electrochemical signals generated from interactions between the aptamers and the target molecules. The DNA aptamer immobilization on the gold electrode was based on the avidin-biotin interaction. The cyclic voltametry (CV) and square wave voltametry (SWV) values were measured to evaluate the chemical binding to aptamer. When 17beta-estradiol interacted with the DNA aptamer, the current decreased due to the interference of bound 17beta-estradiol with the electron flow produced by a redox reaction between ferrocyanide and ferricyanide. In the negative control experiments, the current decreased only mildly due to the presence of other chemicals.

Aptamers, Nucleotide↗
PubMed2006

Construction of segregated arrays of multiple donor and acceptor units using a dendritic scaffold: remarkable dendrimer effects on photoinduced charge separation.

Dendritic molecules appended with multiple zinc porphyrin units (DPm, m [number of zinc porphyrin units] = 6, 12, and 24) trap bipyridine compounds carrying multiple fullerene units (Py2Fn, n [number of C60 units] = 1-3), affording coordination complexes DPm superset Py2Fn having a photoactive layer consisting of spatially segregated donor and acceptor arrays on their surface. Complexes DPm superset Py2Fn are stable enough (K [average binding affinity] = 1.1 x 10(6)-4.4 x 10(6) M(-1) in CHCl3 at 25 degrees C) to be isolated by gel permeation chromatography. UHV-STM microscopy enables clear visualization of a petal-like structure of DP12 superset Py2F3. Photoexcitation of the zinc porphyrin units in DPm superset Py2Fn results in a zinc porphyrin-to-fullerene electron transfer to generate a charge separation. The charge-separation rate constant (kCS) in CH2Cl2 at 20 degrees C increases from 0.26 x 10(10) to 2.3 x 10(10) s(-1) upon increment of m and n, whereas the charge-recombination rate constant (kCR) remains almost unchanged at 4.5 x 10(6)-6.7 x 10(6) s(-1). Consequently, DP24 supersetPy2F3 furnishes the largest ratio of kCS/kCR (3400) among the family.

Dendrimers↗
PubMed2006

A directly fused tetrameric porphyrin sheet and its anomalous electronic properties that arise from the planar cyclooctatetraene core.

Oxidation of a directly meso-meso linked cyclic porphyrin tetramer 2 gave a porphyrin sheet 3. The symmetric square structure of 3 is indicated by its simple 1H NMR spectrum that exhibits only two signals for the porphyrin beta-protons. The absorption spectrum of 3 displays characteristic Soret-like broad bands and weak Q-bands, and its magnetic circular dichroism (MCD) spectrum exhibits a negative Faraday A term at the 762 nm band as a rare case, indicating the absorption as a transition from a nondegenerate level to a degenerate level. A slightly longer S1-state (1.1 ps) and smaller TPA cross section (2750 GM) than a tetrameric linear porphyrin tape also indicate its unique electronic properties. The porphyrin sheet 3 forms stable 1:2 complexes with guest molecules G1 and G2, whose 1H NMR spectra exhibit remarkable downfield shifts for the guest protons that are located just above the cyclooctatetraene (COT) core of 3, whereas the imidazolyl protons bound to the zinc(II) porphyrin local cores are observed at slightly upfield positions. These results have been qualitatively accounted for in terms of the presence of a strong paratropic ring current around the COT core that propagates through the whole pi-electronic network of 3, hence competing with and cancelling the weak diatropic ring currents of the local zinc(II) porphyrins. This explanation was supported by DFT calculation performed at the GIAO-B3LYP/6-31G level, which indicated large positive NICS values within the COT core and small NICS values within the local zinc(II) porphyrins.

Journal Article↗
PubMed2006

Giant porphyrin wheels with large electronic coupling as models of light-harvesting photosynthetic antenna.

Starting from a 1,3-phenylene-linked diporphyrin zinc(II) complex 2ZA, repeated stepwise Ag(I)-promoted coupling reactions provided linear oligomers 4ZA, 6ZA, 8ZA, and 12ZA. The intramolecular cyclization reaction of 12ZA under dilute conditions (1x10(-6) M) gave porphyrin ring C12ZA with a diameter of approximately 35 A in 60% yield. This synthetic strategy has been applied to a 1,3-phenylene-linked tetraporphyrin 4ZB to provide 8ZB, 12ZB, 16ZB, 24ZB, and 32ZB. The intramolecular coupling reaction of 24ZB gave a larger 24-mer porphyrin ring C24ZB with a diameter of approximately 70 A in 34% yield. These two large porphyrin rings were characterized by means of 1H NMR spectroscopy, matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectroscopy, UV-visible spectroscopy, gel permeation chromatography (GPC) analysis, and scanning tunneling microscopy (STM) techniques. The STM images of C12ZA reveal largely circular structures, whereas those of C24ZB exhibit mostly ellipsoidal shapes, indicating more conformational flexibility of C24ZB. Similar to the case of C12ZA, the efficient excitation energy transfer along the ring has been confirmed for C24ZB by using the time-correlated single-photon counting (TCSPC) and picosecond transient absorption anisotropy (TAA) measurements, and occurs with a rate of (35 ps)(-1) for energy hops between neighboring tetraporphyrin subunits. Collectively, the present work provides an important step for the construction of large cyclic-arranged porphyrin arrays with ample electronic interactions as a model of light-harvesting antenna.

Light-Harvesting Protein Complexes↗
PubMed2006

Novel DNA nano-patterning design method utilizing poly-L-lysine patterning by nanoimprint lithography.

The DNA properties have been deliberated to comprehend new functional bio-devices. However there are few reports on DNA nano-patterning to make them. Therefore, we have tried DNA nano-patterning by using a nanoimprint process. A substrate coated with a poly-L-lysine was heated at 120 degrees C for 5 min in atmosphere, and nanoimprint carried out at 120 degrees C, 6 MPa, 5 min, and we applied 1 mg/ml DNA solution on the substrate and immobilized with the poly-L-lysine. Finally the substrate was washed at twice in water and at once in hot water intensely. DNA lines that consist of lines at about 700 nm as line width was obtain, and the very fine lines correspond to convex patterns of the mold surface. These results suggest that the imprint would make the poly-L-lysine reform by exposing it under high pressure and high temperature. Therefore since DNA is immobilized with the amino group in the poly-L-lysine, a lot of amino group would expose on the surface by the imprint from the balk, and would be patterned DNA.

Adsorption↗
PubMed2006

Atomic force microscopy observation of highly arrayed phospholipid bilayer vesicle on a gold surface.

Tapping mode atomic force microscopy (TM-AFM) imaging of a phospholipid bilayer vesicle (liposome) immobilized on a gold surface was performed to investigate morphologies of the electrode surfaces produced through application of three different sample preparation methods. We compared both methods from a morphological viewpoint using TM-AFM images. Liposomes, composed of zwitterionic and anionic phospholipids, were prepared by extrusion. Results indicate that the surface with immobilized L1-liposome, which was fabricated by the amino coupling method, seemed to form large amounts of aggregated or fused liposomes. In contrast, L2-liposome-containing 1-octadecanthiol that was directly attached on the gold surface using thiol-gold binding force was immobilized as a uniform surface topology without liposome aggregation. Finally, we attempted to arrange individual L3-liposome, prepared by mixing zwitterionic and anionic phospholipids, onto the gold layer by electron-beam (e-beam) lithography technique. A third method, L3-liposome formation on the sensor surface, is greatly anticipated for biosensor applications.

Biosensing Techniques↗
PubMed2006

Atomic force microscopic observation of Escherichia coli ribosomes in solution.

Ribosomes of Escherichia coli were visualized in buffer solution by atomic force microscopy (AFM). A series of time-dependent AFM images showed that ribosomes spontaneously adsorb on mica. Although ribosomes observed in air are forced to flatten on the surface, the height of ribosomal particles obtained under a physiological buffer solution is 21.8+/-0.5 nm, which is consistent with the ideal diameter. We succeeded in observing single ribosomes in a near-native condition.

Escherichia coli↗
PubMed2005

Electron-molecular-vibration coupling for small polarons in DNAs.

Within a tight-binding electron-phonon interacting model, we calculated the spectrally resolved polaron binding energy between electrons and phonons and between holes and phonons on poly(dA).poly(dT) and poly(dG).poly(dC).Poly(dA).Poly(dT) is a DNA where one single strand consists only of adenine(A) and the other single strand consists only of thymine(T), while Poly(dG).Poly(dC) is a DNA where one single strand consist only of guanine(G) and the other of cytosine(C). We found that the polaron binding energies of poly(dA).poly(dT) were larger than those of poly(dG).poly(dC), and that the polaron binding energy and the electrical conductance were strongly temperature dependent. These findings agree well with the current experimental data. We concluded that small polaron hopping occurs by a conduction mechanism on the DNA molecules examined.

Binding Sites↗
PubMed2005

Soft lithographic patterning of supported lipid bilayers onto a surface and inside microfluidic channels.

We present simple soft lithographic methods for patterning supported lipid bilayer (SLB) membranes onto a surface and inside microfluidic channels. Micropatterns of polyethylene glycol (PEG)-based polymers were fabricated on glass substrates by microcontact printing or capillary moulding. The patterned PEG surfaces have shown 97 +/- 0.5% reduction in lipid adsorption onto two dimensional surfaces and 95 +/- 1.2% reduction inside microfluidic channels in comparison to glass control. Atomic force microscopy measurements indicated that the deposition of lipid vesicles led to the formation of SLB membranes by vesicle fusion due to hydrophilic interactions with the exposed substrate. Furthermore, the functionality of the patterned SLBs was tested by measuring the binding interactions between biotin (ligand)-labeled lipid bilayer and streptavidin (receptor). SLB arrays were fabricated with spatial resolution down to approximately 500 nm on flat substrate and approximately 1 microm inside microfluidic channels, respectively.

Dimethylpolysiloxanes↗
PubMed2005

Main-chain dominated amyloid structures demonstrated by the effect of high pressure.

It has been suggested that, while the globular native forms of proteins are a side-chain-dominated compact structure evolved by pursuing a unique fold with optimal packing of amino acid residues, amyloid fibrils are a main-chain-dominated structure with an extensive hydrogen bond network. To address this issue, the effects of hydrostatic pressure on amyloid fibrils of beta2-microglobulin (beta2-m), involved in dialysis-related amyloidosis, were studied. A systematic analysis at various pressures and concentrations of guanidine hydrochloride conducted by monitoring thioflavin T fluorescence, light-scattering, and tryptophan fluorescence revealed contrasting conformational changes occurring consecutively: first, a pressure-induced reorganization of fibrils and then a pressure-induced unfolding. The changes in volume as well as the observed structural changes indicate that the beta2-m amyloid fibrils under ambient pressure are less tightly packed with a larger number of cavities, consistent with the main-chain-dominated amyloid structure. Moreover, the amyloid structure without optimal packing will enable various isoforms to form, suggesting the structural basis of multiple forms of amyloid fibrils in contrast to the unique native-fold.

Amyloid↗
PubMed2005

Seeding-dependent propagation and maturation of amyloid fibril conformation.

Recent studies of amyloid fibrils have focused on the presence of multiple amyloid forms even with one protein and their propagation by seeding, leading to conformational memory. To establish the structural basis of these critical features of amyloid fibrils, we used the amyloidogenic fragment Ser20-Lys41 (K3) of beta2-microglobulin, a protein responsible for dialysis-related amyloidosis. In 20% (v/v) 2,2,2-trifluoroethanol and 10 mM HCl (pH approximately 2), K3 peptide formed two types of amyloid-like fibrils, f218 and f210, differing in the amount of beta-sheet as measured by circular dichroism spectroscopy and Fourier transform infrared spectroscopy. Atomic force microscopy showed that the fibril with a larger amount of beta-sheet (f210) is thinner and longer. Both fibrils were reproduced by seeding, showing the template-dependent propagation of a fibril's conformation. However, upon repeated self-seeding, f218 fibrils were gradually transformed into f210 fibrils, revealing the conformational maturation. The observed maturation can be explained fully by a competitive propagation of two fibrils. The maturation of amyloid fibrils might play a role during the development of amyloidosis.

Amino Acid Sequence↗
PubMed2005

Structural studies reveal that the diverse morphology of beta(2)-microglobulin aggregates is a reflection of different molecular architectures.

Amyloid deposition accompanies over 20 degenerative diseases in human, including Alzheimer's, Parkinson's, and prion diseases. Recent studies revealed the importance of other type of protein aggregates, e.g., non-specific aggregates, protofibrils, and small oligomers in the development of such diseases and proved their increased toxicity for living cells in comparison with mature amyloid fibrils. We carried out a comparative structural analysis of different monomeric and aggregated states of beta(2)-microglobulin, a protein responsible for hemodialysis-related amyloidosis. We investigated the structure of the native and acid-denatured states, as well as that of mature fibrils, immature fibrils, amorphous aggregates, and heat-induced filaments, prepared under various in vitro conditions. Infrared spectroscopy demonstrated that the beta-sheet compositions of immature fibrils, heat-induced filaments and amorphous aggregates are characteristic of antiparallel intermolecular beta-sheet structure while mature fibrils are different from all others suggesting a unique overall structure and assembly. Filamentous aggregates prepared by heat treatment are of importance in understanding the in vivo disease because of their stability under physiological conditions, where amyloid fibrils and protofibrils formed at acidic pH depolymerize. Atomic force microscopy of heat-induced filaments represented a morphology similar to that of the low pH immature fibrils. At a pH close to the pI of the protein, amorphous aggregates were formed readily with association of the molecules in native-like conformation, followed by formation of intermolecular beta-sheet structure in a longer time-scale. Extent of the core buried from the solvent in the various states was investigated by H/D exchange of the amide protons.

Amyloid↗
PubMed2005

Single molecule visualization of coordination-assembled porphyrin macrocycles reinforced with covalent linkings.

Coordination-assembled porphyrin macrocycles reinforced with covalent bondings were deposited on a metal surface by a pulse injection method, and their scanning tunneling microscopy (STM) images were recorded under ultrahigh vacuum conditions at liquid nitrogen temperature. The decamer ring consisting of 30 porphyrins gave clear circular STM images with hollow structure, whereas that without covalent linking did not give clear circular images, showing that covalent linking of the coordination pairs by ring-closing metathesis reaction was effective to reinforce the supramolecular structure on a metal surface. This strategy will be applicable to a variety of supramolecular assemblies.

Journal Article↗
PubMed2005

Amperometric immunosensor for direct detection based upon functional lipid vesicles immobilized on nanowell array electrode.

An original electrochemical immunosensor has now been developed that is based upon the spontaneous immobilization of biotinylated, functional lipid vesicles (FLVs) on a polymeric resist layer. An electrode was fabricated utilizing a form of electron-beam (e-beam) that has been used to fabricate 200 nm (nanoscale) wells in the resist layer covering of the gold electrode. The stability of adhered FLVs upon the nanowell (NW) electrode was observed by atomic force microscopy (AFM). From these observations, we were able to determine that the assembled FLVs primarily adhered as individual molecules, that is, without the aggregation or fusion noted in earlier designs. Additionally, these immobilized FLVs demonstrated clearly defined redox activity in electrochemical measurements. Streptavidin, biotinylated capture antibody, and target proteins were consequently injected in order to set up the immunoassay environment. Electrochemical immunoassay experimentation was performed on the NW array electrode with model proteins, such as human serum albumin (HSA) and carbonic anhydrase from bovine (CAB). We observed a notable current decrease, following the redox path, interrupted by the target HSA, indicating the binding of the capture antibody with the target antigen. On the basis of these results, we propose a new type of immunosensor incorporating this mechanism of spontaneous immobilization of FLVs.

Electrochemistry↗